Candidate SNP markers of changes in the expression levels of the human <i>SCN9A</i> gene as a hub gene for pain generation, perception, response and anesthesia

In this work, we for the first time performed a comprehensive bioinformatics analysis of 568 human genes that, according to the NCBI Gene database as on September 15, 2024, were associated with pain generation, perception and anesthesia. The SCN9A gene encoding the sodium voltage-gated channel α sub...

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Main Authors: P. A. Dotsenko, K. A. Zolotareva, R. A. Ivanov, I. V. Chadaeva, N. L. Podkolodnyy, V. A. Ivanisenko, P. S. Demenkov, S. A. Lashin, M. P. Ponomarenko
Format: Article
Language:English
Published: Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders 2025-01-01
Series:Вавиловский журнал генетики и селекции
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Online Access:https://vavilov.elpub.ru/jour/article/view/4403
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author P. A. Dotsenko
K. A. Zolotareva
R. A. Ivanov
I. V. Chadaeva
N. L. Podkolodnyy
V. A. Ivanisenko
P. S. Demenkov
S. A. Lashin
M. P. Ponomarenko
author_facet P. A. Dotsenko
K. A. Zolotareva
R. A. Ivanov
I. V. Chadaeva
N. L. Podkolodnyy
V. A. Ivanisenko
P. S. Demenkov
S. A. Lashin
M. P. Ponomarenko
author_sort P. A. Dotsenko
collection DOAJ
description In this work, we for the first time performed a comprehensive bioinformatics analysis of 568 human genes that, according to the NCBI Gene database as on September 15, 2024, were associated with pain generation, perception and anesthesia. The SCN9A gene encoding the sodium voltage-gated channel α subunit 9 and expressed in sensory neurons for transferring signals to the central nervous system about tissue damage was the only one involved in all the processes of interest at once as a hub gene. First, with our tool called OrthoWeb, we estimated the phylostratigraphic age indices (PAIs) for each of the genes, that is, identified the taxon of the most recent common ancestor of the organisms for which that gene has been sequenced. The mean PAI for all genes under study, including SCN9A as a hub gene for pain generation, perception, response and anesthesia, was ‘4’. On the evolutionary scale by the Kyoto Encyclopedia of Genes and Genomes (KEGG), the ancestor is the phylum Chordata, some of the most ancient of which evolved the central and the peripheral nervous system. Next, with our tool called ANDSystem, we found that phosphorylation of ion channels is a centerpiece in pain generation, perception, response and anesthesia, on which the efficiency of signal transduction from the peripheral to the central system depends. This conclusion was consistent with literature data on a key role an efficient signal transduction from the peripheral to the central system from the peripheral to the central system for adjusting the human circadian rhythm through detection of a change from the dark of night to the light of day and for identification of the direction of the source of sound by auditory brainstem nuclei, for generating the response to cold stress and for physical coordination. 21 candidate SNP marker of significant SCN9A over- and underexpression. Finally, the ratio of SCN9A upregulating to downregulating SNPs was compared to that for all known human genes estimated by the 1000 Genomes Project Consortium. It was found that SCN9A as a hub gene for pain generation, perception, pain response and anesthesia is acted on by natural selection against its downregulation, to keep the nervous system highly informed on the status of the organism and the environment.
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spelling doaj-art-4b0dfb9cc3494a91925c3a4c5b7b479d2025-02-01T09:58:14ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592025-01-0128880882110.18699/vjgb-24-891516Candidate SNP markers of changes in the expression levels of the human <i>SCN9A</i> gene as a hub gene for pain generation, perception, response and anesthesiaP. A. Dotsenko0K. A. Zolotareva1R. A. Ivanov2I. V. Chadaeva3N. L. Podkolodnyy4V. A. Ivanisenko5P. S. Demenkov6S. A. Lashin7M. P. Ponomarenko8Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University; Kurchatov Genomic Center of ICG SB RASInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of ICG SB RASInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Institute of Computational Mathematics and Mathematical Geophysics of the Siberian Branch of the Russian Academy of SciencesInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University; Kurchatov Genomic Center of ICG SB RASInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State UniversityInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of ICG SB RASIn this work, we for the first time performed a comprehensive bioinformatics analysis of 568 human genes that, according to the NCBI Gene database as on September 15, 2024, were associated with pain generation, perception and anesthesia. The SCN9A gene encoding the sodium voltage-gated channel α subunit 9 and expressed in sensory neurons for transferring signals to the central nervous system about tissue damage was the only one involved in all the processes of interest at once as a hub gene. First, with our tool called OrthoWeb, we estimated the phylostratigraphic age indices (PAIs) for each of the genes, that is, identified the taxon of the most recent common ancestor of the organisms for which that gene has been sequenced. The mean PAI for all genes under study, including SCN9A as a hub gene for pain generation, perception, response and anesthesia, was ‘4’. On the evolutionary scale by the Kyoto Encyclopedia of Genes and Genomes (KEGG), the ancestor is the phylum Chordata, some of the most ancient of which evolved the central and the peripheral nervous system. Next, with our tool called ANDSystem, we found that phosphorylation of ion channels is a centerpiece in pain generation, perception, response and anesthesia, on which the efficiency of signal transduction from the peripheral to the central system depends. This conclusion was consistent with literature data on a key role an efficient signal transduction from the peripheral to the central system from the peripheral to the central system for adjusting the human circadian rhythm through detection of a change from the dark of night to the light of day and for identification of the direction of the source of sound by auditory brainstem nuclei, for generating the response to cold stress and for physical coordination. 21 candidate SNP marker of significant SCN9A over- and underexpression. Finally, the ratio of SCN9A upregulating to downregulating SNPs was compared to that for all known human genes estimated by the 1000 Genomes Project Consortium. It was found that SCN9A as a hub gene for pain generation, perception, pain response and anesthesia is acted on by natural selection against its downregulation, to keep the nervous system highly informed on the status of the organism and the environment.https://vavilov.elpub.ru/jour/article/view/4403humantbpsnppromoterhub gene<i>scn9a</i>expression changepain generationpain perceptionpain responseanesthesia
spellingShingle P. A. Dotsenko
K. A. Zolotareva
R. A. Ivanov
I. V. Chadaeva
N. L. Podkolodnyy
V. A. Ivanisenko
P. S. Demenkov
S. A. Lashin
M. P. Ponomarenko
Candidate SNP markers of changes in the expression levels of the human <i>SCN9A</i> gene as a hub gene for pain generation, perception, response and anesthesia
Вавиловский журнал генетики и селекции
human
tbp
snp
promoter
hub gene
<i>scn9a</i>
expression change
pain generation
pain perception
pain response
anesthesia
title Candidate SNP markers of changes in the expression levels of the human <i>SCN9A</i> gene as a hub gene for pain generation, perception, response and anesthesia
title_full Candidate SNP markers of changes in the expression levels of the human <i>SCN9A</i> gene as a hub gene for pain generation, perception, response and anesthesia
title_fullStr Candidate SNP markers of changes in the expression levels of the human <i>SCN9A</i> gene as a hub gene for pain generation, perception, response and anesthesia
title_full_unstemmed Candidate SNP markers of changes in the expression levels of the human <i>SCN9A</i> gene as a hub gene for pain generation, perception, response and anesthesia
title_short Candidate SNP markers of changes in the expression levels of the human <i>SCN9A</i> gene as a hub gene for pain generation, perception, response and anesthesia
title_sort candidate snp markers of changes in the expression levels of the human i scn9a i gene as a hub gene for pain generation perception response and anesthesia
topic human
tbp
snp
promoter
hub gene
<i>scn9a</i>
expression change
pain generation
pain perception
pain response
anesthesia
url https://vavilov.elpub.ru/jour/article/view/4403
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